Molecular structure files

In most programs, it is still possible to input a geometry manually in an ASCII input file. If the geometry is already in a file but of the wrong format, there are several utilities for converting molecular structure files. The most popular of these is the Babel program, which is described in Appendix A. 

CODESSA reads molecular structure files or output files created by other software packages as the starting point for QSAR analysis. It can import computational results from AMPAC, MOPAC, and Gaussian as well as structures in a number of common formats. 

Gund, P., Wipke, W.T., Iangridge, R. Computer searching of a molecular structure file for pharmacophoric patterns. Comput. Chem. Res. Educ. Technol. 1974, 3, 5-21. 

New SQL functions and data types can be used to extend a relational database. This is explained in Chapter 10 using PostgreSQL as an example. Ways in which three-dimensional molecular structures can be stored are examined in Chapter 11. This chapter also advocates using an RDBMS instead of molecular structure files and shows how this transition might be accomplished. 

Chapter 13 shows sample applications that might be developed to produce a registry of compounds for use within a company or project. A set of utility functions is discussed that allows molecular structure files to be imported into a database and used in various ways. 

It would be possible to create tables using columns to store the atomic symbols and bond information found in molecular structure files, reflecting the column style format of the file itself. Instead, a SMILES representation of this valence bond information is preferred. SMILES is a compact text string containing the same information as the columns of atom symbols and bonds. It can also be used directly in the search functions described in earlier chapters. It is desirable to parse the molecular properties in molecular structure files in order to store them in data columns for possible searching... 

In a molecular structure file, an atom record typically contains all of the information about that atom the atomic number or symbol, the charge, coordinates, etc. When such a file is parsed into a SMILES string and an array of coordinates, it is important to be able to associate the proper coordinate with the proper atom. The use of canonical SMILES ensures this. Because canonical SMILES defines a unique order of the atoms in a molecule, that order is used to store the coordinates. Later sections of this chapter will discuss ways in which atomic coordinates might be stored in columns of a table. 

There are many programs available to parse the various molecular structure file format. OpenBabel is an open-source program that can read many file formats and produce a SMILES representation of molecular structure. There are many other commercial products that can do this as well. In the following examples, the OpenBabel/plpythonu implementation of molfile parsing will be used. This was introduced in Chapter 10. The code to define the necessary functions is shown in the Appendix. 

A traditional client program reads from a molecular structure file and performs some computation that depends on the molecular structural data. This read(file) function reads particular columns or fields from the file. A different function would be necessary for each type of file format. A traditional client program can be modified to read molecular structure data from... 

The previous section shows how molecular structures stored in an RDBMS can be made available to client programs that traditionally read molecular structure files. The advantage of storing molecular structures in an RDBMS is that the information can be used from within the database, as well as by external clients. For example, it would be possible to search a table of molecular structures for three-dimensional overlap, much like it might be searched for substructure match. Of course, such search functions need to be written and installed as extensions to an RDBMS, just like the matches functions was done for substructure searches. This section shows some possible ways this might be accomplished. 

Gund P, Wipke WT, Langridge R. Computer searching of a molecular structure file for pharmacophic patterns. Proceedings of International Conference On Computers in Chemical Research and Education, Ljubljana, July, 1974 5-21. 

Fortunately, attempts in the scientific community to set standards for molecular structure files are beginning to gain momentum. Ultimately, the developers and vendors of software will heed the users. Standards will be adopted because it is in the best interest of everyone concerned. 

One of the few examples of commercially available retrieval systems encompassing both compounds and reactions is Molecular Design s microcomputer-based ChemBase system. It saves molfiles (molecular structure files) separately from its reaction file without any elaborate linkages between the files. This makes it rather difficult to move information between the files and requires the conversion of a molfile to move it in or out of a reaction file. Additionally, searching a compound structure for where it appears in a reaction is not a simple operation. Lastly, reaction sites are neither identified nor searchable. These limitations could be overcome if the reaction site could be associated with the molfiles or reaction files stored for searching. 

As a foundation for comparing the SRP RNAs in three dimensions, we used the human SRP RNA model, generated earlier with ERNA-3D (9). Next, we focused on the SRP RNA of M. jannaschii to take advantage of the large number base pairs compounded into helical sections 5bcd, 5gh, 5ij, and 6bc. A simple textual input file was generated to contain the M. Jannaschii SRP RNA sequence, information about the paired residues, and about positions of the helical sections. The positions of the helical sections were copied from the PDB-formatted (18) molecular structure file of the human SRP RNA model (9). 

P. Gund, W. T. Wipke, and R. Langridge, Comput. Chem. Res., Educ., Technol., 3,5 (1974). Computer Searching of a Molecular Structure File for Pharmacophoric Patterns. 

One way to input molecular structure of the new component is to enter individual atoms and bonds. However, a simpler way is to import the molecular structure from other component databanks. A very useful resource is the NIST (National Institute of Standards and Technology) Chemistry WebBook. The information for this new component is shown in Figure 3.66. Click the molecular structure file, 2d Mol file, and save in a known directory with a given file name. The next step is to go to Molecular Structure of EMC under Properties and Click Import Structure to import this file into Aspen Plus (see Fig. 3.67). After this step, ask Aspen Plus to calculate bonds by clicking Calculate Bonds. The graphical structure of EMC is successfully imported into Aspen Plus as shown in Figure 3.68. 

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